Bioinformatics publications
-
CyanoCyc Cyanobacterial Web Portal
CyanoCyc is a web portal that integrates an exceptionally rich database collection of information about cyanobacterial genomes with an extensive suite of bioinformatics tools.
-
The Omics Dashboard for Interactive Exploration of Metabolomics and Multi-Omics Data
The Omics Dashboard is a software tool for interactive exploration and analysis of metabolomics, transcriptomics, proteomics, and multi-omics datasets.
-
The EcoCyc Database (2023)
The long-term goal of the project is to describe the complete molecular catalog of the E. coli cell, as well as the functions of each of its molecular parts, to…
-
BioCyc: Metabolic Pathway Databases and Informatics Tools
This article describes a coordinated set of bioinformatics databases and software tools designed to solve multiple problems faced by metabolic engineers and microbiologists related to metabolic pathways.
-
Reviewing Knowledgebase and Database Grant Proposals in the Life Sciences: The Role of Innovation
This article offers thoughts on reviewing grant proposals for biological knowledgebases and databases (KDs) in the hope of aiding grant reviewers and applicants in addressing the issue of innovation.
-
Pathway Tools Management of Pathway/Genome Data for Microbial Communities
The Pathway Tools software provides a suite of capabilities for storing and analyzing collections of genomic and metabolic information.
-
Metabolic Modeling with MetaFlux
The MetaFlux software supports creating, executing, and solving quantitative metabolic flux models using flux balance analysis (FBA).
-
The EcoCyc Database in 2021
This article highlights recent improvements to the curated data in the areas of metabolism, transport, DNA repair, and regulation of gene expression.
-
The BioCyc Metabolic Network Explorer
The Metabolic Network Explorer is a new addition to the BioCyc.org website and the Pathway Tools software suite that supports the interactive exploration of metabolic networks.
-
Pathway Size Matters: The Influence of Pathway Granularity on Over-Representation (Enrichment) Statistics
We show that alternative pathway definitions can alter enrichment p -values by up to nine orders of magnitude, whereas statistical corrections typically alter enrichment p -values by only two orders…
-
Leveraging Curation Among Escherichia coli Pathway/Genome Databases Using Ortholog-Based Annotation Propagation
We have developed a method to automatically propagate multiple types of curated knowledge from genes and proteins in one genome database to their orthologs in uncurated databases for related strains,…
-
Pathway Tools Visualization of Organism-Scale Metabolic Networks
We have developed bioinformatics software tools that automatically generate a full metabolic-network diagram for an organism, and that enable searching and analyses of the network.